The Capitan Formation originated as a linear organic bank rather than a barrier reef along the Guadalupe Mountain trend. Frame-building organisms, reef cores, and reef-derived detritus or talus are conspicuously absent in the Capitan Formation. Further, the long-standing practice of separating topographically a reef massive (core) unit above and a reef talus or breccia unit below is discounted because the same limestone lithology (mixed organic-skeletal facies) is present above and below the topographic break.

The Capitan Formation can be divided into a lower dolomite unit and an upper limestone unit. In both units, the dominant facies is characterized by much silt- and sand-size skeletal debris and to lesser extent by a wide assortment of in-place, generally scattered, invertebrate fossils. Sediment-binding algae probably were important in trapping and binding skeletal debris, thereby permitting the thick buildup of Capitan carbonate sediment.